Source code for fastr.utils.cmd.run

# Copyright 2011-2014 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import argparse
import fastr.execution.executionscript
from fastr.utils.cmd import add_parser_doc_link


[docs]def get_parser(): parser = argparse.ArgumentParser(description="Execute a job or network from commandline.") parser.add_argument('network', metavar='NETWORKFILE', type=str, help='File of the network to execute') return parser
[docs]def create_network_parser(network): parser = argparse.ArgumentParser(description="Execute the {} Network".format(network.id)) for source in network.sourcelist: parser.add_argument('--{}'.format(source), metavar=source.upper(), required=True, nargs='*', help='Source data for {}'.format(source)) for sink in network.sinklist: parser.add_argument('--{}'.format(sink), metavar=sink.upper(), required=True, help='The Sink output specification for {}'.format(sink)) return parser
[docs]def main(): """ Run a Network from the commandline """ # No arguments were parsed yet, parse them now parser = add_parser_doc_link(get_parser(), __file__) args, unknown_args = parser.parse_known_args() network = fastr.api.Network.load(args.network) network_parser = create_network_parser(network._parent) network_args = vars(network_parser.parse_args(unknown_args)) # Split data in Source and Sink data source_data = {} for source in network.sourcelist: source_data[source] = network_args[source] sink_data = {} for sink in network.sinklist: sink_data[sink] = network_args[sink] fastr.log.info('Source data: {}'.format(source_data)) fastr.log.info('Sink data: {}'.format(sink_data)) network.execute(source_data, sink_data)
if __name__ == '__main__': main()